Re: [Biopython] Planning the Biopython 1.84 release

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Please resume merging pull requests, still a formal release notice to write
but otherwise done. Note another new issue came up with the PDF output:

https://github.com/biopython/biopython/issues/4764

Peter


On Fri, Jun 28, 2024 at 5:20=E2=80=AFAM Peter Cock <[email protected]=
om>
wrote:

> Nearly there, the Biopython 1.84 release is on PyPI now.
>
> One open question, what should I call the new PDF for the archive here:
> https://github.com/biopython/DIST/tree/gh-pages/docs/tutorial
>
> Historically it was based on Tutorial.pdf and Tutorial.html, but now
> we have Biopython_doc.pdf reflecting the fact this combines the old
> "Tutorial and Cookbook" and the "API Documentation".
>
> md5 checksums:
>
> $ md5sum biopython-1.84.tar.gz biopython-1.84*.whl
> 92e639d2f3627759f12f0d000131c24d  biopython-1.84.tar.gz
> 2d121260dc6acc5d0abbd5f9f32bc70a
>  biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl
> 6819b274d250b5a9d4dea7bdf40bf77b
>  biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl
> af78716df05afd11a550d92faf647cf5
>  biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l
> 4e81ecdff61d2fac377af1958bfbcdc5  biopython-1.84-cp310-cp310-win32.whl
> dd6a434bf1c1c7af66ef890b0d43d398  biopython-1.84-cp310-cp310-win_amd64.wh=
l
> d471893df22b6198924f48b96c5c86fc
>  biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl
> 54fe09ad0c76ed1d522369470456699b
>  biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl
> d47b8a1d0c5dc6fc66ba6c86773d02f9
>  biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l
> 1b9e7f5024a47bc17d1f122494bc4ec9  biopython-1.84-cp311-cp311-win32.whl
> 45c924f7245b1a136304d0a17b6e64f6  biopython-1.84-cp311-cp311-win_amd64.wh=
l
> 2296549d1a73b86968bf8af049a3ffde
>  biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl
> c2b8d56c26ac5ef11dcf07097dbdf6da
>  biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl
> 8ce75d3e2935829082c7e6fbe5e6eaab
>  biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l
> a2fae5789c1d911948c55c63efe5b72c  biopython-1.84-cp312-cp312-win32.whl
> 1a72201772c299dd6a4c4f4e825ea829  biopython-1.84-cp312-cp312-win_amd64.wh=
l
> 1e268eff35f32b7c0c829296a0527a45
>  biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl
> 249a1c92cbed3a645cc17878564baacf
>  biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl
> a2bdc8f02dd45e6616b5385138d1b8ff
>  biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 310b7676c7ad2528a6ee10f97471f9c0  biopython-1.84-cp39-cp39-win32.whl
> 76161614a81816de4d206b45aa02eb87  biopython-1.84-cp39-cp39-win_amd64.whl
>
> And sha-256 checksums:
>
> $ sha256sum  biopython-1.84.tar.gz biopython-1.84*.whl
> 60fbe6f996e8a6866a42698c17e552127d99a9aab3259d6249fbaabd0e0cc7b4
>  biopython-1.84.tar.gz
> 3c8beded38884abae4c74cb6ce54142da670273fd0b2919bd0f84f6e34d3056b
>  biopython-1.84-cp310-cp310-macosx_10_9_x86_64.whl
> b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72ac98b479f8d8fe4
>  biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl
> 2dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4
>  biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l
> 4f39b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad
>  biopython-1.84-cp310-cp310-win32.whl
> 9e3f7476fd81f31e048965d7be2826f018686e870d96870f440b609002953954
>  biopython-1.84-cp310-cp310-win_amd64.whl
> 2d4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4
>  biopython-1.84-cp311-cp311-macosx_10_9_x86_64.whl
> c792508988fc3ccf18eaae2a826c9cd97f1c27fb55bb87bdce6a101fee9f5a0c
>  biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl
> 894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2170753d101a13e7585ff4
>  biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l
> 7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467706603f
>  biopython-1.84-cp311-cp311-win32.whl
> 2cb8e839ab472244b6082635ad1df67c94c05df0bd02a023103ed00ea66c4d20
>  biopython-1.84-cp311-cp311-win_amd64.whl
> ba58a6d76288333c5f178a426116953fa68204bd0cfc401694087dd4f96d0059
>  biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl
> ee3566f6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae
>  biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl
> 61765b71f84814a1eeb55ab222f43330aa7ad3e55ab91e8b444706149c67a281
>  biopython-1.84-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.wh=
l
> 52b6098f47d6b90fc8a5e8579b81ee50047e9108f0976e69c891ae0c4817e42d
>  biopython-1.84-cp312-cp312-win32.whl
> ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f7396c
>  biopython-1.84-cp312-cp312-win_amd64.whl
> f4c1c9ad7da9eaf8d8f4515bf931a7f6548a468e7ef29b8429e31aaff2d95f4c
>  biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl
> 9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce5626ffa8976d170da7
>  biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl
> 7b69d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089
>  biopython-1.84-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> 25f4ef193a307e403eb532e8f060b818e2d75f65803a2b0f4e645b0cae131b4e
>  biopython-1.84-cp39-cp39-win32.whl
> b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4813376855b479118
>  biopython-1.84-cp39-cp39-win_amd64.whl
>
>
> On Fri, Jun 28, 2024 at 2:46=E2=80=AFAM Peter Cock <p.j.a.cock@googlemail=
.com>
> wrote:
>
>> I am working on the release now, forgot I didn't have LaTeX on this
>> machine
>> which we still need for a PDF version of the Tutorial (this is the first
>> release
>> to use Sphinx and RST for the Tutorial, rather than LaTeX directly).
>>
>> Please don't update the master branch until the release is done.
>>
>> Peter
>>
>> On Wed, Jun 26, 2024 at 11:37=E2=80=AFAM Peter Cock <p.j.a.cock@googlema=
il.com>
>> wrote:
>>
>>> I've been working on this (as have Michiel, Jo=C3=A3o, and others), and=
 still
>>> hope to do the release very soon.
>>>
>>> Touch wood the numpy 2.0.0 work is done. Right now I'm fixing a minor
>>> regression with the new scipy 1.14.0 release, and hoping there are no m=
ore
>>> surprises!
>>>
>>> Peter
>>>
>>> On Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock <p.j.a.cock@googlema=
il.com>
>>> wrote:
>>>
>>>> Hello all,
>>>>
>>>> I would have liked to tackle the release sooner, but things have been
>>>> busy at work. However, I will be on leave soon and should be able to t=
ackle
>>>> the Biopython 1.84 in early June.
>>>>
>>>> That will be about six months worth of changes, including dropping
>>>> Python 3.8 support and deprecating Python 3.9 support.
>>>>
>>>> It is worth noting this coincides with the release of NumPy 2.0. We
>>>> have lots of code using NumPy, including C code, which was a major con=
cern
>>>> as there are C API breakages with NumPy 2.0. However, rather than the =
full
>>>> NumPy C API, we're only using the buffer API designed for interoperabi=
lity,
>>>> so I believe that does not affect us. What does affect us are changes =
to
>>>> the NumPy scalar repr output, which means a lot of the documentation t=
ests
>>>> in Biopython 1.63 fail. We have addressed those already, and the tests=
 now
>>>> pass on a recent NumPy v1 and on the v2 release candidate. i.e. I am n=
ot
>>>> aware of any blocking issues relating to NumPy for our next release.
>>>>
>>>> Are there any outstanding issues which the community feels need to be
>>>> addressed prior to our release?
>>>>
>>>> Thanks,
>>>>
>>>> Peter
>>>>
>>>

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<div dir=3D"ltr"><div>Please resume merging pull requests, still a formal r=
elease notice to write</div><div>but otherwise done. Note another new issue=
 came up with the PDF output:</div><div><br></div><div><a href=3D"https://g=
ithub.com/biopython/biopython/issues/4764">https://github.com/biopython/bio=
python/issues/4764</a></div><div><br></div><div>Peter</div><div><br></div><=
/div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">O=
n Fri, Jun 28, 2024 at 5:20=E2=80=AFAM Peter Cock &lt;<a href=3D"mailto:p.j=
[email protected]">[email protected]</a>&gt; wrote:<br></div><=
blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-l=
eft:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>Near=
ly there, the Biopython 1.84 release is on PyPI now.</div><div><br></div><d=
iv>One open question, what should I call the new PDF for the archive here:<=
/div><div><a href=3D"https://github.com/biopython/DIST/tree/gh-pages/docs/t=
utorial" target=3D"_blank">https://github.com/biopython/DIST/tree/gh-pages/=
docs/tutorial</a></div><div><br></div><div>Historically it was based on Tut=
orial.pdf and Tutorial.html, but now</div><div>we have Biopython_doc.pdf re=
flecting the fact this combines the old</div><div>&quot;Tutorial and Cookbo=
ok&quot; and the &quot;API Documentation&quot;.<br></div><div><br></div><di=
v>md5 checksums:</div><div><br></div><div>$ md5sum biopython-1.84.tar.gz bi=
opython-1.84*.whl<br>92e639d2f3627759f12f0d000131c24d =C2=A0biopython-1.84.=
tar.gz<br>2d121260dc6acc5d0abbd5f9f32bc70a =C2=A0biopython-1.84-cp310-cp310=
-macosx_10_9_x86_64.whl<br>6819b274d250b5a9d4dea7bdf40bf77b =C2=A0biopython=
-1.84-cp310-cp310-macosx_11_0_arm64.whl<br>af78716df05afd11a550d92faf647cf5=
 =C2=A0biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_6=
4.whl<br>4e81ecdff61d2fac377af1958bfbcdc5 =C2=A0biopython-1.84-cp310-cp310-=
win32.whl<br>dd6a434bf1c1c7af66ef890b0d43d398 =C2=A0biopython-1.84-cp310-cp=
310-win_amd64.whl<br>d471893df22b6198924f48b96c5c86fc =C2=A0biopython-1.84-=
cp311-cp311-macosx_10_9_x86_64.whl<br>54fe09ad0c76ed1d522369470456699b =C2=
=A0biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl<br>d47b8a1d0c5dc6fc66ba=
6c86773d02f9 =C2=A0biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylin=
ux2014_x86_64.whl<br>1b9e7f5024a47bc17d1f122494bc4ec9 =C2=A0biopython-1.84-=
cp311-cp311-win32.whl<br>45c924f7245b1a136304d0a17b6e64f6 =C2=A0biopython-1=
.84-cp311-cp311-win_amd64.whl<br>2296549d1a73b86968bf8af049a3ffde =C2=A0bio=
python-1.84-cp312-cp312-macosx_10_9_x86_64.whl<br>c2b8d56c26ac5ef11dcf07097=
dbdf6da =C2=A0biopython-1.84-cp312-cp312-macosx_11_0_arm64.whl<br>8ce75d3e2=
935829082c7e6fbe5e6eaab =C2=A0biopython-1.84-cp312-cp312-manylinux_2_17_x86=
_64.manylinux2014_x86_64.whl<br>a2fae5789c1d911948c55c63efe5b72c =C2=A0biop=
ython-1.84-cp312-cp312-win32.whl<br>1a72201772c299dd6a4c4f4e825ea829 =C2=A0=
biopython-1.84-cp312-cp312-win_amd64.whl<br>1e268eff35f32b7c0c829296a0527a4=
5 =C2=A0biopython-1.84-cp39-cp39-macosx_10_9_x86_64.whl<br>249a1c92cbed3a64=
5cc17878564baacf =C2=A0biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl<br>a2=
bdc8f02dd45e6616b5385138d1b8ff =C2=A0biopython-1.84-cp39-cp39-manylinux_2_1=
7_x86_64.manylinux2014_x86_64.whl<br>310b7676c7ad2528a6ee10f97471f9c0 =C2=
=A0biopython-1.84-cp39-cp39-win32.whl<br>76161614a81816de4d206b45aa02eb87 =
=C2=A0biopython-1.84-cp39-cp39-win_amd64.whl</div><div><br></div><div>And s=
ha-256 checksums:</div><div><br></div><div>$ sha256sum =C2=A0biopython-1.84=
.tar.gz biopython-1.84*.whl<br>60fbe6f996e8a6866a42698c17e552127d99a9aab325=
9d6249fbaabd0e0cc7b4 =C2=A0biopython-1.84.tar.gz<br>3c8beded38884abae4c74cb=
6ce54142da670273fd0b2919bd0f84f6e34d3056b =C2=A0biopython-1.84-cp310-cp310-=
macosx_10_9_x86_64.whl<br>b51ef31bfb79872a182a85b4113625e1b553c024bb1586c72=
ac98b479f8d8fe4 =C2=A0biopython-1.84-cp310-cp310-macosx_11_0_arm64.whl<br>2=
dc2e77490725060330003f73b6b7d5172f8bc160f180de5877a2e899ad999d4 =C2=A0biopy=
thon-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>4f3=
9b38e7625c33384954130d90f19984e91cb5af64e2fb128603359f86884ad =C2=A0biopyth=
on-1.84-cp310-cp310-win32.whl<br>9e3f7476fd81f31e048965d7be2826f018686e870d=
96870f440b609002953954 =C2=A0biopython-1.84-cp310-cp310-win_amd64.whl<br>2d=
4ed30aebd96b4aadeb1f04adce92795c696f5bd56d1fd45517b89059918dd4 =C2=A0biopyt=
hon-1.84-cp311-cp311-macosx_10_9_x86_64.whl<br>c792508988fc3ccf18eaae2a826c=
9cd97f1c27fb55bb87bdce6a101fee9f5a0c =C2=A0biopython-1.84-cp311-cp311-macos=
x_11_0_arm64.whl<br>894ee7533cca7f5f9769e2595fbe7b0dba5018f39a2170753d101a1=
3e7585ff4 =C2=A0biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2=
014_x86_64.whl<br>7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467=
706603f =C2=A0biopython-1.84-cp311-cp311-win32.whl<br>2cb8e839ab472244b6082=
635ad1df67c94c05df0bd02a023103ed00ea66c4d20 =C2=A0biopython-1.84-cp311-cp31=
1-win_amd64.whl<br>ba58a6d76288333c5f178a426116953fa68204bd0cfc401694087dd4=
f96d0059 =C2=A0biopython-1.84-cp312-cp312-macosx_10_9_x86_64.whl<br>ee3566f=
6dc3acf20e238540daf896f0af20cff531521bf41fdf5143f73e209ae =C2=A0biopython-1=
.84-cp312-cp312-macosx_11_0_arm64.whl<br>61765b71f84814a1eeb55ab222f43330aa=
7ad3e55ab91e8b444706149c67a281 =C2=A0biopython-1.84-cp312-cp312-manylinux_2=
_17_x86_64.manylinux2014_x86_64.whl<br>52b6098f47d6b90fc8a5e8579b81ee50047e=
9108f0976e69c891ae0c4817e42d =C2=A0biopython-1.84-cp312-cp312-win32.whl<br>=
ecff2fcf5da29b600474c0bfcdbbac0f98b25e22fe60a853d0ee798c00f7396c =C2=A0biop=
ython-1.84-cp312-cp312-win_amd64.whl<br>f4c1c9ad7da9eaf8d8f4515bf931a7f6548=
a468e7ef29b8429e31aaff2d95f4c =C2=A0biopython-1.84-cp39-cp39-macosx_10_9_x8=
6_64.whl<br>9fbd4b67d3e71b0d716a1712ab8b4e57981c6549ba17ce5626ffa8976d170da=
7 =C2=A0biopython-1.84-cp39-cp39-macosx_11_0_arm64.whl<br>7b69d59f9a762c5bb=
5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089 =C2=A0biopython-1.84-cp39-c=
p39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl<br>25f4ef193a307e403eb53=
2e8f060b818e2d75f65803a2b0f4e645b0cae131b4e =C2=A0biopython-1.84-cp39-cp39-=
win32.whl<br>b64575363bb2344073c949fd69a0bf3ea015b447aa1494e4813376855b4791=
18 =C2=A0biopython-1.84-cp39-cp39-win_amd64.whl</div><div><br></div></div><=
br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Fri,=
 Jun 28, 2024 at 2:46=E2=80=AFAM Peter Cock &lt;<a href=3D"mailto:p.j.a.coc=
[email protected]" target=3D"_blank">[email protected]</a>&gt; wrote=
:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.=
8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"lt=
r"><div>I am working on the release now, forgot I didn&#39;t have LaTeX on =
this machine</div><div>which we still need for a PDF version of the Tutoria=
l (this is the first release</div><div>to use Sphinx and RST for the Tutori=
al, rather than LaTeX directly).</div><div><br></div><div>Please don&#39;t =
update the master branch until the release is done.<br></div><div><br></div=
><div>Peter<br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" =
class=3D"gmail_attr">On Wed, Jun 26, 2024 at 11:37=E2=80=AFAM Peter Cock &l=
t;<a href=3D"mailto:[email protected]" target=3D"_blank">p.j.a.cock=
@googlemail.com</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" s=
tyle=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);pad=
ding-left:1ex"><div dir=3D"ltr"><div>I&#39;ve been working on this (as have=
 Michiel,=C2=A0Jo=C3=A3o,  and others), and still hope to do the release ve=
ry soon.</div><div><br></div><div>Touch wood the numpy 2.0.0 work is done. =
Right now I&#39;m fixing a minor regression with the new scipy 1.14.0 relea=
se, and hoping there are no more surprises!<br></div><div><br></div><div>Pe=
ter<br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D=
"gmail_attr">On Wed, May 22, 2024 at 9:39=E2=80=AFPM Peter Cock &lt;<a href=
=3D"mailto:[email protected]" target=3D"_blank">p.j.a.cock@googlema=
il.com</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"m=
argin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left=
:1ex"><div dir=3D"ltr"><div>Hello all,</div><div><br></div><div>I would hav=
e liked to tackle the release sooner, but things have been busy at work. Ho=
wever, I will be on leave soon and should be able to tackle the Biopython 1=
.84 in early June.</div><div><br></div><div>That will be about six months w=
orth of changes, including dropping Python 3.8 support and deprecating Pyth=
on 3.9 support.<br></div><div><br></div><div>It is worth noting this coinci=
des with the release of NumPy 2.0. We have lots of code using NumPy, includ=
ing C code, which was a major concern as there are C API breakages with Num=
Py 2.0. However, rather than the full NumPy C API, we&#39;re only using the=
 buffer API designed for interoperability, so I believe that does not affec=
t us. What does affect us are changes to the NumPy scalar repr output, whic=
h means a lot of the documentation tests in Biopython 1.63 fail. We have ad=
dressed those already, and the tests now pass on a recent NumPy v1 and on t=
he v2 release candidate. i.e. I am not aware of any blocking issues relatin=
g to NumPy for our next release.</div><div><br></div><div>Are there any out=
standing issues which the community feels need to be addressed prior to our=
 release?</div><div><br></div><div>Thanks,<br></div><br><div>Peter<br></div=
></div>
</blockquote></div>
</blockquote></div>
</blockquote></div>
</blockquote></div>

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